> A question concerning consensus sequences: how do you handle gaps? N > (as I understood it) does not allow a gap. Is there a way to encode a > "might be gap here, or A or G"?
If the input is a multiple sequence alignment then you could count frequencies at each position and take the most frequently occurring nucleotide. For each position you could count a conservation score. Andreas _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
